Fix testing importing modules in containers

lib/galaxy/tool_util/deps/mulled/get_tests.py

@@ -12,6 +12,7 @@ from glob import glob
 from typing import (
     Any,
     Dict,
+    List,
     Optional,
 )
 
@@ -26,6 +27,7 @@ except ImportError:
     UndefinedError = Exception  # type: ignore[assignment,misc]
 
 from galaxy.util import unicodify
+from galaxy.util.commands import argv_to_str
 from .util import (
     get_files_from_conda_package,
     MULLED_SOCKET_TIMEOUT,
@@ -66,6 +68,7 @@ def get_commands_from_yaml(yaml_content: bytes) -> Optional[Dict[str, Any]]:
         return None
 
     # need to know what scripting languages are needed to run the container
+    package_tests["import_lang"] = "python -c"  # python by default
     try:
         requirements = list(meta_yaml["requirements"]["run"])
     except (KeyError, TypeError):
@@ -77,8 +80,6 @@ def get_commands_from_yaml(yaml_content: bytes) -> Optional[Dict[str, Any]]:
                 break
             # elif ... :
             # other languages if necessary ... hopefully python and perl should suffice though
-        else:  # python by default
-            package_tests["import_lang"] = "python -c"
     return package_tests
 
 
@@ -260,6 +261,15 @@ def main_test_search(
     return {"container": container}
 
 
+def import_test_to_command_list(import_lang: str, import_: str) -> List[str]:
+    if import_lang == "python -c":
+        return ["python", "-c", f"import {import_}"]
+    elif import_lang == "perl -e":
+        return ["perl", "-e", f"use {import_}"]
+    else:
+        raise ValueError(f"Unsupported import_lang '{import_lang}'")
+
+
 def hashed_test_search(
     container, recipes_path=None, deep=False, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"
 ):
@@ -294,7 +304,8 @@ def hashed_test_search(
     for container in containers:
         tests = main_test_search(container, recipes_path, deep, anaconda_channel, github_repo)
         package_tests["commands"] += tests.get("commands", [])  # not a very nice solution but probably the simplest
+        # Given that this could be a mix of Python and Perl packages, translate imports to commands
         for imp in tests.get("imports", []):
-            package_tests["imports"].append(f"{tests['import_lang']} 'import {imp}'")
+            package_tests["commands"].append(argv_to_str(import_test_to_command_list(tests["import_lang"], imp)))
 
     return package_tests

lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py

@@ -17,6 +17,7 @@ from typing import (
 from galaxy.util import unicodify
 from .get_tests import (
     hashed_test_search,
+    import_test_to_command_list,
     main_test_search,
 )
 
@@ -77,7 +78,10 @@ def singularity_container_test(
 
                 for imp in test.get("imports", []):
                     try:
-                        check_output(exec_command + [test["import_lang"], f"import {imp}"], stderr=subprocess.STDOUT)
+                        check_output(
+                            exec_command + import_test_to_command_list(test["import_lang"], imp),
+                            stderr=subprocess.STDOUT,
+                        )
                     except subprocess.CalledProcessError as e:
                         errors.append({"import": imp, "output": unicodify(e.output)})
                         test_passed = False

test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py

@@ -1,11 +1,8 @@
 import os
-from typing import (
-    Any,
-    Dict,
-)
 
 import pytest
 
+from galaxy.tool_util.deps.mulled.get_tests import main_test_search
 from galaxy.tool_util.deps.mulled.mulled_update_singularity_containers import (
     docker_to_singularity,
     get_list_from_file,
@@ -38,19 +35,12 @@ def test_docker_to_singularity(tmp_path) -> None:
 @external_dependency_management
 @pytest.mark.skipif(not which("singularity"), reason="requires singularity but singularity not on PATH")
 def test_singularity_container_test(tmp_path) -> None:
-    tests: Dict[str, Dict[str, Any]] = {
-        "pybigwig:0.1.11--py36_0": {
-            "imports": ["pyBigWig"],
-            "commands": ['python -c "import pyBigWig; assert(pyBigWig.numpy == 1); assert(pyBigWig.remote == 1)"'],
-            "import_lang": "python -c",
-        },
-        "samtools:1.0--1": {
-            "commands": ["samtools --help"],
-            "import_lang": "python -c",
-            "container": "samtools:1.0--1",
-        },
-        "yasm:1.3.0--0": {},
-    }
+    containers = [
+        "pybigwig:0.3.22--py36h54a71a5_0",  # test Python imports
+        "samtools:1.0--1",
+        "yasm:1.3.0--0",  # test missing tests
+    ]
+    tests = {container: main_test_search(container) for container in containers}
     for n in tests.keys():
         docker_to_singularity(n, "singularity", tmp_path, no_sudo=True)
     results = singularity_container_test(
@@ -59,5 +49,5 @@ def test_singularity_container_test(tmp_path) -> None:
         tmp_path,
     )
     assert "samtools:1.0--1" in results["passed"]
-    assert results["failed"][0]["imports"] == ["pyBigWig"]
+    assert "pybigwig:0.3.22--py36h54a71a5_0" in results["passed"]
     assert "yasm:1.3.0--0" in results["notest"]